证明:$(1)$∵四边形$ABCD$是平行四边形,
∴$AD=BC,AD// BC,$
∴$∠ ABC+∠ BAD=180°,$
∵$AF// BE,$
∴$∠ EBA+∠ BAF=180°,$
∴$∠ CBE=∠ DAF,$同理得$∠ BCE=∠ ADF.$
$ $在$△ BCE$和$△ ADF_{中},$
$\begin {cases}∠ CBE=∠ DAF \\BC=AD\\∠ BCE=∠ ADF\end {cases}$
∴$△ BCE≌△ ADF(\mathrm {ASA}).$
$ (2) $∵点$E$在$□ ABCD$的内部,
∴$S_{△ BEC}+S_{△ AED}=\frac {1}{2}S_{□ ABCD},$
$ $由$(1)$知$△ BCE≌△ ADF,$
∴$S_{△ BCE}=S_{△ ADF},$
∴$S_{四边形AEDF}=S_{△ ADF}+S_{△ AED}=S_{△ BEC}+S_{△ AED}=\frac {1}{2}S_{□ ABCD}.$
∵$□ ABCD$的面积为$6,$
∴四边形$AEDF $的面积为$3.$